scholarly journals Noncovalent Complexes of Cyclodextrin with Small Organic Molecules: Applications and Insights into Host–Guest Interactions in the Gas Phase and Condensed Phase

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4048
Author(s):  
Jae-ung Lee ◽  
Sung-Sik Lee ◽  
Sungyul Lee ◽  
Han Bin Oh
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Solution Phase ◽  
Condensed Phases ◽  
Valuable Insight ◽  
Noncovalent Complexes ◽  
Separation Science ◽  
X Ray Crystallography ◽  
Theoretical Evidence ◽  
Guest Chemistry

Cyclodextrins (CDs) have drawn a lot of attention from the scientific communities as a model system for host–guest chemistry and also due to its variety of applications in the pharmaceutical, cosmetic, food, textile, separation science, and essential oil industries. The formation of the inclusion complexes enables these applications in the condensed phases, which have been confirmed by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, and other methodologies. The advent of soft ionization techniques that can transfer the solution-phase noncovalent complexes to the gas phase has allowed for extensive examination of these complexes and provides valuable insight into the principles governing the formation of gaseous noncovalent complexes. As for the CDs’ host–guest chemistry in the gas phase, there has been a controversial issue as to whether noncovalent complexes are inclusion conformers reflecting the solution-phase structure of the complex or not. In this review, the basic principles governing CD’s host–guest complex formation will be described. Applications and structures of CDs in the condensed phases will also be presented. More importantly, the experimental and theoretical evidence supporting the two opposing views for the CD–guest structures in the gas phase will be intensively reviewed. These include data obtained via mass spectrometry, ion mobility measurements, infrared multiphoton dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations.

Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study

2020 ◽  
Vol 19 (06) ◽  
pp. 2050014
Author(s):  
Mahendiraprabu Ganesan ◽  
Selvarengan Paranthaman
Keyword(s):  
Gas Phase ◽  
Amyloid Beta ◽  
Density Functional ◽  
Conformational Transition ◽  
Intermolecular Hydrogen Bond ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Secondary Structures ◽  
Conformational Flexibility ◽  
Solution Phase

Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].

scholarly journals Carrier dynamics and the role of surface defects: Designing a photocatalyst for gas-phase CO2 reduction

2016 ◽  
Vol 113 (50) ◽  
pp. E8011-E8020 ◽  
Author(s):  
Laura B. Hoch ◽  
Paul Szymanski ◽  
Kulbir Kaur Ghuman ◽  
Le He ◽  
Kristine Liao ◽  
...  
Keyword(s):  
Photocatalytic Activity ◽  
Excited State ◽  
Oxygen Vacancy ◽  
Band Gap ◽  
Gas Phase ◽  
Density Functional ◽  
Carrier Dynamics ◽  
Valuable Insight ◽  
Relaxation Dynamics ◽  
Excitation Energies

In2O3-x(OH)y nanoparticles have been shown to function as an effective gas-phase photocatalyst for the reduction of CO2 to CO via the reverse water–gas shift reaction. Their photocatalytic activity is strongly correlated to the number of oxygen vacancy and hydroxide defects present in the system. To better understand how such defects interact with photogenerated electrons and holes in these materials, we have studied the relaxation dynamics of In2O3-x(OH)y nanoparticles with varying concentration of defects using two different excitation energies corresponding to above-band-gap (318-nm) and near-band-gap (405-nm) excitations. Our results demonstrate that defects play a significant role in the excited-state, charge relaxation pathways. Higher defect concentrations result in longer excited-state lifetimes, which are attributed to improved charge separation. This correlates well with the observed trends in the photocatalytic activity. These results are further supported by density-functional theory calculations, which confirm the positions of oxygen vacancy and hydroxide defect states within the optical band gap of indium oxide. This enhanced understanding of the role these defects play in determining the optoelectronic properties and charge carrier dynamics can provide valuable insight toward the rational development of more efficient photocatalytic materials for CO2 reduction.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Highly Electron-Deficient Pyridinium-Nitrones for Rapid and Tunable Inverse-Electron-Demand Strain-Promoted Alkyne-Nitrone Cycloaddition to Bicyclo[6.1.0]nonyne

2019 ◽  
Author(s):  
Praveen Gunawardene ◽  
Wilson Luo ◽  
Alexander M. Polgar ◽  
John F. Corrigan ◽  
Mark Workentin
Keyword(s):  
Density Functional Theory ◽  
Reaction Kinetics ◽  
Density Functional ◽  
Functional Theory ◽  
X Ray ◽  
Inverse Electron Demand ◽  
X Ray Crystallography ◽  
Electron Demand

<div> <div> <p>Highly accelerated inverse-electron-demand strain-promoted alkyne-nitrone cycloaddition (IED SPANC) between a sta- ble cyclooctyne (bicyclo[6.1.0]nonyne (BCN)) and nitrones delocalized into a Cα-pyridinium functionality is reported, with the most electron-deficient “pyridinium-nitrone” displaying among the most rapid cycloadditions to BCN that is currently reported. Density functional theory (DFT) and X-ray crystallography are explored to rationalize the effects of N- and Cα-substituent modifications at the nitrone on IED SPANC reaction kinetics and the overall rapid reactivity of pyridinium-delocalized nitrones.</p> </div> </div>

Investigation of Adsorption Effect of Carbon Monoxide on Coniine: A DFT Study

2021 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Mehrnoosh Khaleghian ◽  
Marina Murashko ◽  
Mahin Ahmadianarog ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Adsorption Effect ◽  
Chemical Shift Tensors ◽  
Solvent Water ◽  
Donor And Acceptor ◽  
Before And After ◽  
Electron Donor And Acceptor

: For the first time in the present study, the non-bonded interaction of the Coniine (C8H17N) with carbon monoxide (CO) was investigated by density functional theory (DFT/M062X/6-311+G*) in the gas phase and solvent water. The adsorption of the CO over C8H17N was affected on the electronic properties such as EHOMO, ELUMO, the energy gap between LUMO and HOMO, global hardness. Furthermore, chemical shift tensors and natural charge of the C8H17N and complex C8H17N/CO were determined and discussed. According to the natural bond orbital (NBO) results, the molecule C8H17N and CO play as both electron donor and acceptor at the complex C8H17N/CO in the gas phase and solvent water. On the other hand, the charge transfer is occurred between the bonding, antibonding or nonbonding orbitals in two molecules C8H17N and CO. We have also investigated the charge distribution for the complex C8H17N/CO by molecular electrostatic potential (MEP) calculations using the M062X/6-311+G* level of theory. The electronic spectra of the C8H17N and complex C8H17N/CO were calculated by time dependent DFT (TD-DFT) for investigation of the maximum wavelength value of the C8H17N before and after the non-bonded interaction with the CO in the gas phase and solvent water. Therefore, C8H17N can be used as strong absorbers for air purification and reduce environmental pollution.

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 328
Author(s):  
Raquel Álvarez-Vidaurre ◽  
Alfonso Castiñeiras ◽  
Antonio Frontera ◽  
Isabel García-Santos ◽  
Diego M. Gil ◽  
...  
Keyword(s):  
Density Functional ◽  
Glycolic Acid ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Functional Theory ◽  
Molecular Systems ◽  
X Ray Crystallography ◽  
Hydroxycarboxylic Acids ◽  
Non Covalent Interactions ◽  
Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

scholarly journals On the Many-Body Expansion of an Interaction Energy of Some Supramolecular Halogen-Containing Capsules

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4431
Author(s):  
Jiří Czernek ◽  
Jiří Brus
Keyword(s):  
Density Functional ◽  
Condensed Phases ◽  
Multicomponent Mixtures ◽  
Many Body ◽  
Symmetric Form ◽  
Functional Theory ◽  
Emergent Features ◽  
The Many ◽  
Surprising Fact ◽  
Dimethyl Benzene

A tetramer model was investigated of a remarkably stable iodine-containing supramolecular capsule that was most recently characterized by other authors, who described emergent features of the capsule’s formation. In an attempt to address the surprising fact that no strong pair-wise interactions between any of the respective components were experimentally detected in condensed phases, the DFT (density-functional theory) computational model was used to decompose the total stabilization energy as a sum of two-, three- and four-body contributions. This model considers complexes formed between either iodine or bromine and the crucial D4h-symmetric form of octaaryl macrocyclic compound cyclo[8](1,3-(4,6-dimethyl)benzene that is surrounded by arenes of a suitable size, namely, either corannulene or coronene. A significant enthalpic gain associated with the formation of investigated tetramers was revealed. Furthermore, it is shown that the total stabilization of these complexes is dominated by binary interactions. Based on these findings, comments are made regarding the experimentally observed behavior of related multicomponent mixtures.

scholarly journals Selective capture of carbon dioxide from hydrocarbons using a metal-organic framework

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Omid T. Qazvini ◽  
Ravichandar Babarao ◽  
Shane G. Telfer
Keyword(s):  
Carbon Dioxide ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Time Lags ◽  
X Ray Crystallography ◽  
Metal Organic ◽  
Adsorption Of Co ◽  
Short Time ◽  
Organic Framework

AbstractEfficient and sustainable methods for carbon dioxide capture are highly sought after. Mature technologies involve chemical reactions that absorb CO2, but they have many drawbacks. Energy-efficient alternatives may be realised by porous physisorbents with void spaces that are complementary in size and electrostatic potential to molecular CO2. Here, we present a robust, recyclable and inexpensive adsorbent termed MUF-16. This metal-organic framework captures CO2 with a high affinity in its one-dimensional channels, as determined by adsorption isotherms, X-ray crystallography and density-functional theory calculations. Its low affinity for other competing gases delivers high selectivity for the adsorption of CO2 over methane, acetylene, ethylene, ethane, propylene and propane. For equimolar mixtures of CO2/CH4 and CO2/C2H2, the selectivity is 6690 and 510, respectively. Breakthrough gas separations under dynamic conditions benefit from short time lags in the elution of the weakly-adsorbed component to deliver high-purity hydrocarbon products, including pure methane and acetylene.

Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide

2020 ◽  
Vol 22 (9) ◽  
pp. 5057-5069 ◽  
Author(s):  
Jae-ung Lee ◽  
Yeonjoon Kim ◽  
Woo Youn Kim ◽  
Han Bin Oh
Keyword(s):  
Graph Theory ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Reaction Pathway ◽  
Peptide Sequencing ◽  
Phase Reaction ◽  
Functional Theory ◽  
Fragmentation Mechanisms ◽  
Gas Phase Fragmentation

A new approach for elucidating gas-phase fragmentation mechanisms is proposed: graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory (DFT) calculations.

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